New Super Mario Bros., ironically this throw back does mix up the boss formula for the end. Spoilers when you get to Bowser at the end they make it seem like you will battle him as normal, but after you defeat him he grows to giant size and you have to run from him. In fact you have to bait him into breathing fire on certain obstacles so you can pass.
I think that games can come up with new climaxes other than fight a giant guy at the end, especially in platformers the idea of escaping a crumbling structure and leaving the antagonist trapped inside works well, especially if the characters are not intended to be superhuman.
On Uncharted 3 I think Garnett over thought the new ending. Instead I would just have Drake barely beat him to the sap, have him flip out ignite it since he can't have it all to himself and then you have to escape while he chases you shooting at you with a grenade launcher. You can shoot back to slow him, but you loose speed aiming. A nice climax where the bad guy's greed is his undoing.